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DOI: 10.1126/science.1206375, 1091 (2011);334Science

, et al.Douglas H. ErwinSuccess in the Early History of AnimalsThe Cambrian Conundrum: Early Divergence and Later Ecological

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The Cambrian Conundrum: EarlyDivergence and Later EcologicalSuccess in the Early History of AnimalsDouglas H. Erwin,1,2* Marc Laflamme,1 Sarah M. Tweedt,1,3 Erik A. Sperling,4

Davide Pisani,5 Kevin J. Peterson6*

Diverse bilaterian clades emerged apparently within a few million years during the earlyCambrian, and various environmental, developmental, and ecological causes have been proposedto explain this abrupt appearance. A compilation of the patterns of fossil and moleculardiversification, comparative developmental data, and information on ecological feeding strategiesindicate that the major animal clades diverged many tens of millions of years before theirfirst appearance in the fossil record, demonstrating a macroevolutionary lag between theestablishment of their developmental toolkits during the Cryogenian [(850 to 635 million yearsago Ma)] and the later ecological success of metazoans during the Ediacaran (635 to 541 Ma)and Cambrian (541 to 488 Ma) periods. We argue that this diversification involved new formsof developmental regulation, as well as innovations in networks of ecological interaction within

the context of permissive environmental circumstances.

When Charles Darwin published TheOrigin of Species (1), the sudden ap-pearance of animal fossils in the rock

record was one of the more troubling facts hewas compelled to address. He wrote: There isanother and allied difficulty, which is muchgraver. I allude to the manner in which numbersof species of the same group, suddenly appear inthe lowest known fossiliferous rocks (p. 306).Darwin argued that the incompleteness of thefossil record gives the illusion of an explosive

event, but with the eventual discovery of olderand better-preserved rocks, the ancestors ofthese Cambrian taxa would be found. Studiesof Ediacaran and Cambrian fossils continue toexpand the morphologic variety of clades, butthe appearance of the remains and traces of bi-laterian animals in the Cambrian remains abrupt(Fig. 1 and tables S1 and S2).

The fossil record is now supplemented withgeochemical proxies of environmental change; aprecise temporal framework allowing for cor-relation of rocks in different areas of the worldand evaluation of rates of evolutionary and envi-ronmental change; an increasingly rigorous un-derstanding of the phylogenetic relationships

between various living and fossil metazoan cladesand their dates of origin, based largely on mo-lecular sequences; and growing knowledge ofthe evolution of developmental processes throughcomparative studies of living groups. Collectively,these records allow an understanding of the en-vironmental potential, genetic and developmentalpossibility, and ecological opportunity that ex-isted before and during the Cambrian. Here, we provide an updated synthesis (2, 3) of theserecords and thereby a macroevolutionary frame-

work for understanding the Cambrian explosion.Pattern of Animal Diversification

The Cambrian fossil record. The beginning ofthe Cambrian Period dated at 541 T 0.13 millionyears ago (Ma) (4) is defined by the first appear-ance of the trace fossil Treptichnus pedum (5) inthe rock record, representing the first appearanceof bilaterian animals with the ability to makecomplex burrows both horizontally (Fig. 2A)and vertically (6). The earliest skeletal fossils oc-cur in the latest Ediacaran, but the first appear-ance of an array of plates, spines, shells, and otherskeletal elements of bilaterian affinity begins dur-ing the early Cambrian Fortunian Stage (541to ~530 Ma) (7, 8) (Fig. 3). Most of these aredisarticulated elements larger than 2 mm in size,but some complete scleritomes (Fig. 2B) havebeen recovered. They reveal a fauna with con-siderable morphologic and phylogenetic diver-sity and are collectively referred to as the smallshelly fauna (SSF). The earliest SSF are largelyof lophotrochozoan affinities; only in CambrianStage 3 do biomineralized ecdysozoans and deu-terostomes appear (8). Many of the SSF elementsare preserved as phosphate minerals, and theirdiversity peaks in abundant phosphate depos-

its (9). Although Ediacaran phosphate depits are common, they lack SSF, suggesting thbilaterian clades acquired skeletons during Cambrian.

The pattern seen from the skeletal and trafossil record is mirrored by soft-bodied fossfound in exceptionally preserved Cambrian fanas in China, Greenland, Australia, Canada (F2C), and elsewhere. Although many new grou

have been described over the past decade, t pattern of diversification of both body fosand trace fossils has remained largely robustrecompilation (SOM text 1 and table S1) of first occurrences of all metazoan phyla, classand stem-classes (extinct clades) of equivalmorphologic disparity (Fig. 2, D and E) shotheir first occurrences in the latest Ediacar(by 555 Ma), with a dramatic rise over abo25 million years in the first several stages of tCambrian, and continuing into the Ordovic(Figs. 1 and 3 and table S3). However, from early Paleozoic onward there is little additionnew phyla and classes (Fig. 1), and those t

are added are largely artifactual, as they repsent occurrences of taxa with little or no prervation potential (10).

The molecular record. Given the clear snal for an explosive appearance of animal fosils in the early Cambrian (Figs. 1 and 3), mpaleontologists favor a near literal readingthe fossil record, supporting a rapid (~25-millioyear) evolutionary divergence of most animclades near the base of the Cambrian [e.g., (11But teasing apart the mechanisms underlythe Cambrian explosion requires disentanglievolutionary origins from geological first apearances, and the only way to separate the t

is to use a molecular clock (12). Many earlproblems with molecular divergence estimahave been addressed, allowing confident esmates of the robustness of the known geologrecord (13, 14).

Building upon a previously assembled dset (14) and a generally accepted phylogenetree, we estimated divergence times for >1species of animals (alignment available as dabase S1), encompassing all major metazoan cla(Fig. 1, SOM text 2, table S4, figs. S1 to S4, adatabase S2). Although much of the topolois well accepted, including the tripartite divisiof bilaterians into lophotrochozoans, ecdysozoaand deuterostomes and the paraphyletic naturediploblasts with respect to triploblasts (151the paraphyletic nature of sponges is more cotroversial (15, 17). However, the estimated vergence times (SOM text and figs. S5 to S1do not depend on this presumption; they are arobust to the choice of the root prior, the molular clock model, subsampling of the calibratipoints, and relaxation of the bounds of the cbration point intervals themselves (table S4). Athough acoelomorphs have figured prominenin discussions about the reconstruction of anctral bilaterians (18, 19), they are not included

RESEARCHARTICLES

1Department of Paleobiology, MRC-121, National Museumof Natural History, Post Office Box 37012, Washington, DC200137012, USA.

2Santa Fe Institute, 1399 Hyde Park Road,Santa Fe, NM 87501, USA. 3Behavior, Ecology, Evolution andSystematics, University of Maryland, College Park, MD 20742,USA. 4Department of Earth and Planetary Sciences, HarvardUniversity, Cambridge, MA 02138, USA. 5Department of Bi-ology, The National University of Ireland, Maynooth, Kildare,Ireland. 6Department of Biology, Dartmouth College, Hanover,NH 03755, USA.

*To whom correspondence should be addressed. E-mail:[email protected] (D.H.E); [email protected](K.J.P.)

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the analysis owing to their incomplete genesampling and very long branches; moreover, arecent analysis (20) indicates that they may bederived deuterostomes, and thus their only con-tribution to this analysis would be to demonstratethe extent of character loss among some bilat-erian clades (see below).

These molecular estimates suggest that theorigin and earliest diversification of animals oc-curred during the Cryogenian Period. We esti-mate that the last common ancestor of all livinganimals arose nearly 800 Ma and that the stemlineages leading to most extant phyla had evolvedby the end of the Ediacaran (541 Ma). Most

phylum-level crown group divergences occurcoevally between the end of the Ediacaran athe end of the Cambrian (Figs. 1 and 3, larcolored circles). This is the case both for tawith robust fossil records (e.g., echinodermmolluscs, arthropods) and those with sparse fsil records (e.g., nemerteans, nematodes). F

Fig. 1. The origin and diversification of animals as inferred from the geologicand genetic fossil records. The dramatic rise in the number of animal fossils(see scale on left) in the Cambrian relative to the Ediacaran conveys the impactof the Cambrian explosion of animal life. Little high-level morphologicalinnovation occurred during the subsequent 500 million years in that muchof animal disparity, as measured by the Linnean taxonomic ranking, wasachieved early in the radiation. Overlying the geologic record is the patternof animal origination as inferred from the molecular clock. Seven differenthousekeeping genes from 118 taxa were used to generate this chronogram(see SOM 2 for methodological details and database S1). Twenty-four cali-brations (open circles) were used and treated as soft bounds. Divergence timesfor key nodes and their 95% highest posterior intervals are reported in data-

base S2. All estimates appear to be robust to numerous experimental manulations performed to assess whether the results were dependent on tparameters used in the analyses (Materials and Methods, SOM Text 2, and fiS5 to S10). There is general concordance of bilaterian phylum-level crogroups (colored circles; the color of each circle is the same as the corresponing taxonomic bar and label on the far right), with the first appearance of manimal groups at the Ediacaran-Cambrian boundary. In contrast, the originsthe demosponge (dark blue) and cnidarian (yellow) as well as the bilateri(black) and metazoan (gray) crown groups are deep in the Cryogenian. Gological period abbreviations: , Cambrian; O, Ordovician; S, Silurian;Devonian; C, Carboniferous; P, Permian; Tr, Triassic; J, Jurassic; K, CretaceoPe, Paleogene; N, Neogene. A high-resolution image is available in the SO

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taxa with robust fossil records, these coeval orig-ination estimates are concordant with their firstappearances in the rock record (Fig. 3), support-ing both the general accuracy of our relaxed mo-lecular clock analysis and the intuition of manypaleontologists who argued that the known fos-sil record for crown groups of bilaterian phyla islargely robust (11).

Our divergence estimates suggest that crown-group demosponges (Figs. 1 and 3, dark blue

circle) and crown-group cnidarians (yellowcircle)have deep origins, both at nearly 700 Ma. Thesecould represent artifacts, although the former iscorroborated by Cryogenian-age fossil molecules(biomarkers) of demosponges (21) and possiblesponge body fossils reported from the Cryogenian(22). The deep divergence of the cnidarian crowngroup is less easily explained, but the degree ofmolecular divergence among cnidarian classesis roughly equal to the protostome-deuterostomedivergence (23), which is consistent with ourresults.

The Neoproterozoic fossil record. The un-avoidable conclusion from the molecular record

is that precambrian animals are largely stemlineages leading to extant phyla, and that theselineages originated in the Ediacaran (Figs. 1 and

3). Numerous eukaryotic taxa, including the firstexample of multicellularity with complex devel-opment (24), are represented in rocks assignedto the later (i.e.,


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deuterostomes) evolved at least 25 million yearsearlier (Figs. 1 and 3).

In sum, geologic evidence and molecularclock estimates suggest that early animals, no-tably crown-group demosponges and cnidarians,originated during the Cryogenian. Although bi-laterian clades diversified in the Ediacaran, many phylum-level crown groups were not present,appearing first in the Cambrian.

Environmental PotentialVery large geochemical changes have been doc-umented through the Cryogenian and Ediacaran(4547), which have been interpreted as indi-cating substantial changes in redox. Changes inmolybdenum abundance in black shales (48),the iron chemistry of deep-water sediments (49),and potentially other proxies (46) have been in-terpreted as a global signal of increased oxy-genation during the Ediacaran. The extent towhich these signals are truly global, as well asthe magnitude of oxidation, remains uncertain.Animals require oxygen to fuel their metabo-lism, and these geochemical proxies and their

interpretation as markers of redox conditionshave been invoked to explain the lag betweenthe origin of animals and the Cambrian radiationitself (2). In this view, low oxygen in the oceansand diffusive oxygen transport constrained ani-mals to small size, and only with an increase inoxygen levels could organisms evolve larger, three-dimensional body sizes (24, 50), greatly facili-tating their eventual paleontological detection.Thus, although a permissive environment does notexplain innovations in metazoan architecture, itmight facilitate the appearance of large and eco-logically diverse animals in the fossil record.

Genetic and Developmental Possibility

Two findings from comparative genomics andstudies of developmental patterning have dra-matically changed our understanding of the ear-ly evolution of animals. First, whole-genomesequencing of dozens of metazoans has dem-onstrated that any animal requires only about20,000 protein-coding genes for the productionof its essential morphologic architecture (51).Second, much of this protein-coding repertoireespecially the developmental toolkitis con-served throughout all metazoans and is evenfound today among single-celled opisthokonts(24, 5254). The distribution of these genes inextant organisms (SOM text 3) implies thatthis toolkit evolved in a two-step pattern (Fig. 4,left): an initial diversification occurring at thebase of the Metazoa before the split betweensponges and eumetazoans deep in the Cryogenian(and possibly earlier), followed by a pronouncedexpansion at least in some families at the baseof the Eumetazoa during the late Cryogenian(database S3). Thus, the last common ancestorof metazoans, and especially eumetazoans, wasa genetically complex animal possessing all ofthe families of protein-coding genes used dur-ing development, save for the potential absence

of Hox complex genes (55) needed to buildthe plethora of morphological structures foundthroughout the crown group.

Consequently, the morphological simplicityof basal animals, and the great differences inmorphology between sponges and arthropodsor vertebrates, cannot be due to the absence ofthese protein-coding gene families but insteadmust involve differences in the temporal andspatial deployment of these genes and their

regulation. By extension, this includes the costruction of developmental gene regulatory nworks (dGRNs) specific to particular charact(for example, the gut, heart, or appendages). the core of these networks are extremely coserved, highly refractory and recursively wisuites of genes that are crucial for the speccation of many of the characteristic morphogies of major clades (56, 57), and ultimatdefining the developmental morphospace (5

Fig. 3. Detailed stage-level depiction of the animal fossil record as compared to the molecudivergence estimates for 13 different animal lineages. Shown in yellow and blue is the known fossil recof animals at the class and phylum levels, respectively (hatching indicates stem lineages, i.e., lineathat belong to a specific phylumbut not to any ofits living classes); shown in green is the generic recordmacroscopic Ediacara fossils (see scale at bottom). Shown in thick black lines are the known fossil recoof each of these 13 lineages through the Cryogenian-Ordovician (table S1); most lineages make their fappearance in the Cambrian, consistent with the known fossil record of all animals (yellow and bluFurther, the extent of these stratigraphic ranges closely mirrors the molecular estimates for the ageeach of the respective crown groups (colored circles) (see also Fig. 1), highlighting the general accurof the molecular clock. Only cnidarians have an unexpectedly deep crown-group origination as etimated by the molecular clock, as the deep demosponge divergence is apparent from taxon-specibiomarkers (gray bar) (21).


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accessible to a clade. Such networks are likelyto have evolved via intercalary evolution in whichdevelopmental genes providing spatial, tempo-ral, and homeostatic control were inserted intopreexisting simpler dGRN subcircuits (58). Oneexample of genetic intercalation into these dGRNsis the continual evolutionary addition of micro-RNAs (miRNAs). miRNAs encode ~22-nucleotidenoncoding regulatory RNAs that affect the trans-lation of target mRNAs, ultimately contributing

to the maintenance of cellular homeostasis andcellular identity (59) and to the robustness of de-velopmental programs (60). Unlike the mRNAtoolkit, which was largely established before theevolution of bilaterians (Fig. 4, left), miRNAs(database S4) seem to have been continuouslyadded to eumetazoan genomes through time withvery little secondary loss in most taxa (Fig. 4,right) (60). When loss did occur, it seems to havebeen associated with morphological simplifica-tion (20). For example, each of the extant animals put forth as putative biological models for late precambrian animals, including lophotrochozoanflatworms, acoel flatworms, and Xenoturbella

(61), are characterized by extensive secondaryloss of their miRNA complements as comparedto more typical invertebrates like ambulacrariandeuterostomes, crustacean arthropods, and poly-chaete annelids (60). In contrast, large expansionsin the number of miRNA families correlate toincreases in the number of cell types and mor-

phological complexity of animals, as seen, forexample, at the base of the bilaterians and atthe base of the vertebrates (60) (Fig. 4, right).

Whereas there is little difference in the mRNAtoolkit between humans and sea anemones(Fig. 4, left), there is a dramatic difference in themiRNA toolkit between these two taxa (Fig. 4,right). The increasing morphologic complexityand developmental stability of bilaterian lineagesthen likely reflects, at least in part, an increase in

the diversity and number of dGRN subcircuits,including the continued and hierarchical incor- poration of miRNAs into these networks in alineage-specific manner (60). Other potentiallynoteworthy aspects of regulatory control that maybe important in bilaterian diversification are otherforms of RNA regulation, alternative splicing oftranscripts (62), and combinatorial control of en-hancers, but we lack sufficient comparative datato evaluate their role in the diversification of bi-laterian animals. Because the signaling pathwaysand transcription factors important for bilateriandevelopment first appeared among basal metazo-an clades that originated in the Cryogenian, the

advent of elements of the metazoan develop-mental toolkit was a necessary but not sufficientcomponent of the Cambrian explosion. A subtlebut critical change from the views of a decadeago is that the primary developmental contri-bution to the origin of bilaterians lay with theconstruction and elaboration of patterns of de-

velopmental control (56, 57), not additionsthe mRNA developmental toolkit. The tempolag between the initial construction of these nworks and the eventual appearance of bilaterfossils suggests that the solution to the dilemmof the Cambrian explosion lies not solely wthis genomic and developmental potential, binstead must also be found in the ecology of tCambrian radiation itself.

Ecological OpportunitiesEvolutionary radiations are often describedthe invasion ofempty ecological space, bthetransition from the Ediacaran to theCambrinvolved far-reaching changes in benthic aneritic ecosystems and the de novo constrution of complex metazoan ecological netwo(63, 64). Standard models of adaptive radiati(65) involve diversification from a single claand cannot explain the polyphyletic nature, mphological and ecological breadth, or the etended duration of this event. Rather, we identa suite of processes that facilitated the constrution of biodiversity through positive feedba

ecosystem engineering of the environment, pticularly by Cryogenian-Ediacaran sponges alater by burrowing bilaterians, and the formtion of new ecological linkages including tevolution of zooplankton, which connected plagic and benthic systems (64), and the adventmetazoan predation.

Fig. 4. Acquisition andsecondary loss of mes-senger RNAs (mRNAs,left)and microRNAs (miRNAs,right) in selected taxa.One hundred and thirty-

one representative tran-scription factors andsignaling ligands werecoded for eight metazoantaxa (database S3) andmapped onto a widely ac-cepted metazoan topol-ogy (15, 16). The lengthof the branch representsthetotal number of mRNAgenes acquired minus thosethat were lost (scale barrepresents 10 genes to-tal). Much of the devel-opmental mRNA toolkit

was acquired before thelast common ancestor ofcnidarians and bilaterians. This is in contrast to the miRNArepertoire that displays extensive gain of miRNAs in thebilaterian stem lineage after it split from cnidarians. All139 miRNA families known from 22 metazoan specieswere coded (database S4), and similar to the mRNAfigure (left), the length of the branch represents thetotal number of miRNA genes gained at that point minusthose that were secondarily lost (scale bar represents 10genes total). Increases to morphological complexity arecorrelated with increases to the miRNA toolkit (60), andsecondary simplifications in morphology correlate with a relatively high level of secondary miRNA loss (20).

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Ecosystem engineering occurs when the ac-tivities of one or more species modify the phys-ical and/or chemical environment(s), affectingthe flow of energy, nutrients, and other resourcesthrough a network of species (66, 67). This of-ten has important ecological and evolutionaryconsequences (68). The engineering activitieswith the greatest evolutionary implications arethose that affect resource availability. For exam-ple, sponges remove dissolved organic matter and

bacteria from the water column (34) and whenabundant can transfer large volumes of carbonto the sediment, thus changing the geochemistryof the water column. The advent of vertical bur-rowing in the early Cambrian enhanced the oxy-genation of the sediment and microbial primary productivity, providing food for benthic meta-zoans (69).

Predation was an important component ofthe growth of these ecological networks. Thefirst appearance of predatory traces, and bodyfossils of predators, occurs near the Ediacaran-Cambrian transition (70). Animals evolved inresponse to predation pressures by developing

novel defensive mechanisms such as biomin-eralized shells or developing new structuresor capabilities that allowed movement intonew habitats. The origin of predation can be as-sessed by mapping feeding modes onto thetime-calibrated phylogeny (Fig. 3). Given thesimilarities between the sponge feeding cell(choanocyte) and choanoflagellates, the meta-zoan last common ancestor (LCA) was likely amicrophagous suspension feeder, irrespectiveof whether sponges are monophyletic or not.Cnidarians are potential late Cryogenian pred-ators, and the estimated age of their crown group(~687 Ma) is also the minimal estimate for the

evolution of the cnidocyte, the stinging cellsthat enable cnidarians to prey on other animals.However, the ~150-million-year gap betweenthe appearance of the cnidocyte and the esti-mated origin of pancrustaceans (Fig. 1), theirprimary modern prey, raises questions aboutthe nature of early Cryogenian food webs. Cni-darians may have preyed on benthic micro-metazoans, and the correlative innovation oftrue endomesoderm in bilaterians and the cni-docyte in their immediate sister group, the cni-darians, may suggest a coevolutionary responsebetween these two lineages at this relatively earlystage in animal evolution.

Feeding modes along the eumetazoan stemare difficult to polarize (41), but these organismsare unlikely to have been predators, especiallyupon other animals, as bona fide predation doesnot appear to be primitive for any of the threegreat clades of bilaterians. The deuterostomeLCA almost certainly filter-fed using gill slits,as the Chordata, Echinodermata, and Hemichor-data each have filter-feeding representatives intheir basal branches. Within Ecdysozoa, currentphylogenetic analyses suggest that the predomi-nantly detritivorous cycloneuralian worms forma paraphyletic assemblage at the base of the

clade (71, 72), so detritus feeding was likelyprimitive for this group. The diversity of feedingstrategies among the Lophotrochozoa make itdifficult to reconstruct the basal strategy, butbecause carnivorous molluscs and annelids arederived within each respective phylum, theirLCA was unlikely to have been carnivorous either.The only protostome phyla whose crown-groupancestor was likely carnivorous are the chaetog-naths and the nemerteans, and both the fossil

record (73) and molecular clock results (Fig.3) suggest that their ancestor appeared in thelate Ediacaran to early Cambrian. Thus, we seeno evidence for a carnivorous lifestyle during theCryogenian to mid-Ediacaran for any bilaterianlineage. Given that ecology and the physical en-vironment are closely linked, it may be that theorigin of animal carnivory, a metabolically ex-pensive feeding strategy, was driven by increasedoxygenation.

Outlook

Our emerging understanding of early animalhistory shows that evolution is not always re-

lentlessly opportunistic, taking advantage of evo-lutionary novelties as soon as they arise. Rather,the Cambrian explosion involved the construc-tion of historically unique, and uniquely com-plex, feedbacks between biological potential andeco-environmental context, including the oxy-genation of the oceans waters. These feedbacksrelied on networks of gene regulatory interactionthat were established long before the construc-tion of metazoan ecosystems. Because of thislong lag between the origin and eventual eco-logical dominance of clades, data on taxonomicoccurrences alone are insufficient to understandevolutionary dynamics and must be accompa-

nied by data on abundances and ecological im-pact, in addition to accurate and precise estimatesof both evolutionary origin and geological firstappearances. Macroevolutionary lags such asthat which preceded the Cambrian explosionwere not unique to animals, as similar dynamicsseem to underlie plant evolution as well (24).Understanding both early animal and plant evo-lution requires an understanding of the processesthat generate biodiversity and the expansion ofecological networks through deep time.

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Acknowledgments: This work was supported by a NASA

National Astrobiology Institute grant (D.H.E and K.J.P)

supporting M.L., S.M.T., and E.A.S., and a Smithsonian

Institution Fellowship (M.L). E.A.S is also supported by

an Agouron Geobiology Fellowship. K.J.P. is also

supported by the NSF. D.P. is supported by a Science

Foundation Ireland Research Frontier Programme

grant (08/RFP/EOB1595). All molecular analyses were

performed with the computing infrastructures provided

by the Irish Center for High End Computing and

the National University of Ireland Maynooth High

Performance Computing facility. All data used in the

paper are included as files in the SOM. We appreciate

technical assistance from L. Campbell and comments

from P. Donoghue, G. Edgecombe, G. Narbonne,

B. Runnegar, two anonymous reviewers, and the Bio

Class of Dartmouth College (2011).

Supporting Online Materialwww.sciencemag.org/cgi/content/full/334/6059/1091/DC1

Materials and Methods

SOM Text

Figs. S1 to S10

Tables S1 to S6

Databases S1 to S4

References (74169)

9 June 2011; accepted 5 October 2011

10.1126/science.1206375

A Potent and Broad NeutralizingAntibody Recognizes and Penetrates

the HIV Glycan ShieldRobert Pejchal,1* Katie J. Doores,2,3* Laura M. Walker,2* Reza Khayat,1* Po-Ssu Huang,4*Sheng-Kai Wang,5 Robyn L. Stanfield,1 Jean-Philippe Julien,1 Alejandra Ramos,2 Max Crispin,6

Rafael Depetris,7 Umesh Katpally,8 Andre Marozsan,8 Albert Cupo,8 Sebastien Maloveste,9

Yan Liu,10 Ryan McBride,11 Yukishige Ito,12 Rogier W. Sanders,7,13 Cassandra Ogohara,4

James C. Paulson,11 Ten Feizi,10 Christopher N. Scanlan,6 Chi-Huey Wong,5 John P. Moore,7

William C. Olson,8 Andrew B. Ward,1 Pascal Poignard,2,14 William R. Schief,2,4

Dennis R. Burton,2,3 Ian A. Wilson1

The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycanshield. However, several of the recently identified PGT broadly neutralizing antibodies appear tointeract directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs)PGT 127 and 128 with Man9 at 1.65 and 1.29 angstrom resolution, respectively, and glycanbinding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fullyglycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates theglycan shield and recognizes two conserved glycans as well as a short b-strand segment of thegp120 V3 loop, accounting for its high binding affinity and broad specificify. Furthermore, our

data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may bemediated by cross-linking Env trimers on the viral surface.

Viruses have evolved a variety of mech-anisms to escape antibody recognition,many of which involve features of the

viral surface proteins, such as high variability,steric occlusion, and glycan coating. For HIV,the dense shield of glycans (1, 2) that decoratethe viral Env protein was once believed to berefractory to antibody recognition, masking con-served functionally significant protein epitopesfor which greater exposure would result in in-creased susceptibility to antibody neutralization.However, the broadly neutralizing monoclonalantibody (bnmAb) 2G12 and several of the recent-ly described PGTantibodies appear to binddirectlyto the HIV glycan coat. Although carbohydrate-protein interactions are typically weak (3), 2G12recognizes terminal dimannose (Mana1,2Man)moieties on oligomannose glycans, using an un-usual domain-exchanged antibody structure thatcreatesa multivalent binding surface that enhancesthe affinity of the interaction through avidity ef-fects (4). However, although 2G12 neutralizescladeB isolatesbroadly, it is less effective against

other clades, particularly clade C viruses, whichhave a somewhat different oligomannose glycanarrangement than clade B viruses. In contrast,we have recently isolatedsix bnmAbs(PGTs 125to 128, 130, and 131) that bind specifically to theMan8/9 glycans on gp120 and potently neutralizeacross clades (5). PGT 128, the broadest of theseantibodies, neutralizes over 70% of globally cir-culating viruses and is, on average, an order ofmagnitude more potentthan therecently describedPG9, PG16, VRC01, and PGV04 (also known asVRC-PG04) bnmAbs (58) and is two orders ofmagnitude more potent than prototype bnmAbsdescribed earlier (6, 9).

The neutralization potency exhibited by thePGT class of antibodies suggests that they mayprovide protection at relatively low serum con-centrations. Hence, the epitopes recognized bythese antibodies may be good vaccine targets ifappropriate immunogens can be designed.

Crystal structures of PGTs 127 and 128

bound to Man9. To gain a structural understand-ing of the specificity for Man8/9 glycans by

PGTs 127 and 128, we first determined crysstructures of the Fabs of PGTs 127 and 1with a synthetic Man9 glycan lacking the cN-acetylglucosamine (GlcNAc) moieties at 1and 1.29 resolution, respectively (table SThe bound glycan is well ordered, except the terminal mannose residue of the D2 a(Fig. 1 and figs. S1 and S2A). The 127/Man9 a128/Man9 structures showa similar conformat

for the glycan (fig. S1), demonstrating a coserved mode of recognition by these clonally lated antibodies.

Analysis of these crystal structures revethe origin of their specificity for Man8/9 gcans. The terminal mannose residues of bothe D1 and D3 arms, which are only present Man8/9 glycans (Fig. 1B, Fig. 2A, and fig. S2Aare heavily contacted, forming 11 of the 16 tohydrogen-bonding interactions with the antibo(table S2).This specificity for glycans is consent with glycan array data showing bindiof PGT 127 and 128 to Man8 and Man9, bnot to monoglucosylated Man9 N-glycans (f

S3A), and with glycosidase inhibitor specific

1Department of Molecular Biology, Skaggs Institute for Chical Biology, and International AIDS Vaccine Initiative (IANeutralizing Antibody Center, The Scripps Research InstitLa Jolla, CA 92037, USA. 2Department of Immunology Microbial Science and IAVI Neutralizing Antibody CenThe Scripps ResearchInstitute, La Jolla, CA 92037, USA.3RaInstitute of MGH, MIT, and Harvard, Cambridge, MA 021USA. 4Department of Biochemistry, University of WashingSeattle, WA 98195,USA. 5Department of Chemistry, TheScrResearch Institute, La Jolla, CA 92037, USA. 6Oxford Glybiology Institute, Department of Biochemistry, UniversitOxford, South Parks Road, Oxford, OX1 3QU, UK. 7Weill Mcal College of Cornell University, New York, NY 10021, U8Progenics Pharmaceuticals, Tarrytown, NY 10591, USA. 9

oratory of Molecular Microbiology, National Institute of Alleand Infectious Diseases, National Institutes of Health, BetheMD 20892, USA. 10Glycosciences Laboratory, DepartmenMedicine, Imperial College London, Hammersmith CampDu Cane Road, London, W12 0NN, UK. 11Department of Piological Chemistry, The Scripps Research Institute, La Jolla92037, USA. 12RIKEN Advanced Science Institute and ExpatoryResearch for Advanced Technology, Japan ScienceTechnology Agency, 2-1 Hirosawa, Wako, Saitama 351-01Japan. 13Department of Medical Microbiology, Academic Mical Center, Amsterdam, Netherlands. 14International AIDS Vcine Initiative, New York, NY 10038, USA.

*These authors contributed equally to this work.To whom correspondence should be addressed: [email protected] (D.R.B.); [email protected] (I.A.

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